Do novel acidophilic archaeal ammonia oxidisers solve the paradox of nitrification in acid soils?

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Nitrification is an essential process in the cycling of nitrogen throughout the planet. The process consists of the conversion of ammonia to nitrate by two groups of microorganisms. Ammonia oxidisers convert ammonia to nitrite and this is then converted to nitrate by nitrite oxidisers. Although beneficial to some plants, nitrification can have deleterious consequences. Ammonium can be retained in soil but, after conversion to nitrate, it is leached from soil, polluting groundwaters that may be used to supply drinking water. It also contributes to atmospheric pollution, as ammonia oxidation is accompanied by production of nitrous oxide, a potent greenhouse gas that also contributes to destruction of stratospheric ozone. None of the ammonia oxidisers that have been grown in the laboratory can grow at low pH, but nitrification occurs in acid soils and there is actually evidence that rates are slightly greater at low pH. Approximately 30% of the world's soils are acidic (pH less than 5.5), mainly due to microbial activity, including that of nitrifiers. They represent a wide range of natural and managed habitats including forestry, agriculture and grasslands. Acid soils are therefore of great environmental and economic importance and it is important that we understand the mechanisms leading to nitrification in these soils. Several explanations have been proposed to explain ammonia oxidation at low pH, but none provides a full explanation and all are difficult to demonstrate in soil. Traditionally, the most important soil ammonia oxidisers were thought to be bacteria but we now know that the thaumarchaea, another group of abundant soil organisms, can oxidise ammonia. Thaumarchaea are a group within the archaea, a domain of microbial life distinct from the bacteria. Although they resemble bacteria in many ways, they are evolutionarily distinct and were previously thought to be restricted to 'extreme' environments. We recently obtained evidence that two groups of thaumarchaeal ammonia oxidisers are restricted to acid soils, suggesting adaptation to growth at low pH. We then obtained a culture of an organism, Nitrosotalea devanaterra, which is representative of one of the groups and showed it to be a strict, acidophilic ammonia oxidiser that grows only within the pH range 4 - 5.5. At these pH values, ammonia availability will be extremely low, because most will be ionised to ammonium. N. devanaterra must therefore possess unique mechanisms for ammonia oxidation at low pH that enable it to occupy this improbable environmental niche in acid soils. A major aim of the project will therefore be to determine the mechanism by which N. devanaterra grows at low pH. We also aim to obtain a culture of the second group of acidophilic thaumarchaeal ammonia oxidisers, identified in our earlier studies, and to determine whether both groups utilise the same mechanism. Potential mechanisms will be investigated by sequencing and analysing all of the genes in both strains and identifying which genes are expressed when they are growing at low pH. These mechanisms will then be tested in laboratory growth experiments.The second major aim is to determine whether these organisms are actually important in nitrification in acid soils. We will use soil laboratory systems (microcosms) to determine their ability to grow in a range of acid soils and determine whether their growth is associated with ammonia oxidation. We will manipulate soil pH, to determine the influence of pH on their growth and activity, and we will also determine whether the physiological mechanisms that explain growth at low pH in laboratory culture explain growth in acid soils.